Star Trek: Trapped in Darkness
by chisscientist
Summary: When something goes wrong reviving Khan from cryosleep, Khan finds himself in the toughest situation he has ever faced. Alone and injured, can he manage to free himself and his crew from Marcus' hands? AU
1. Chapter 1

Disclaimer: I do not own any form of Star Trek, and am making no money from this. This is purely for my entertainment and that of those reading this. It is primarily based off _Star Trek Into Darkness_, with some influence from TOS for missing information.

**Prolog: What on Earth?**

Ambassador Selek, formerly known as Spock, did a double-take as he scanned the morning news. Wait 60 seconds... was that Khan wearing sunglasses? Half-Vulcan or not, he felt fear grip him even if he chose not to show it.

Unless Spock was completely mistaken that was indeed Khan, along with Admiral Pike, Kirk, young Spock, McCoy, and Carol Marcus. A short distance away stood Admiral Alexander Marcus, wearing handcuffs and an absolutely livid expression. 'Head of Starfleet Under Arrest', the title read.

It looked like this time continuum might be becoming more alternative by the second. He'd better contact young Spock now and find out what was going on - hopefully before Khan was running the Federation.


	2. Oh, the Possibilities

**Chapter One: Oh, the Possibilities!**

When Admiral Marcus first saw Captain Selva's report, he assumed it was a joke. Selva should have known better to send his stupid enthusiasms to Command. Sighing, Admiral Marcus opened the line to Selva, then reached down and picked up a PADD and a couple of bits and pieces that had fallen to the floor. Blasted paperclips.

"Admiral," Captain Selva said, saluting.

"Captain," replied Marcus, "I would appreciate it if you kept April Fool's jokes out of your reports to Starfleet Command."

Selva looked confused for a moment, then replied "Sir, I am not joking. We have indeed found the Botany Bay."

Marcus' jaw started to drop, but he snapped it shut. "I want details," he said. "Now."

The possibilities were staggering, and he wasn't just talking about the things that would have had historians dancing for joy. It had been suspected for decades that some of the Augmented humans had escaped at the end of the Eugenics wars, possibly in that ship. Maybe even Khan, last and greatest of the eugenics tyrants.

The Augments were living weapons, and in the right hands - his hands - they might just be what was needed to end the Klingon menace and properly strengthen Starfleet. He ordered Selva to remove the cryotubes from the Botany Bay and bring them to the Jupiter Section 31 base secretly.

While that order was carried out, Marcus buried himself in all the information he could find on the Augments and the Eugenics Wars. He also called in a historian - Macgivers was her name - to give him as much detail on Khan and the other late-surviving Augments as she could. He got a few descriptions, and even a copy of a badly water-damaged photograph that might be of Khan, although Macgivers wasn't sure. He thanked her and sent her away wondering what the head of Starfleet wanted with the history of such an ancient war.

The information was fascinating, but also disturbing. The Augments were impressive in their abilities, but also in their aggression and ambition. He almost reconsidered the whole idea. The last thing he wanted was the Augments back in power.

But the power wielding them would give him... it was worth a few risks. And it wasn't as if he were going to wake all of them. There was limits to how much trouble one Augment could make. Khan himself was the only one they had any decent information on, so he was the one they'd wake if they could identify him. And since he would have been executed if he had been caught it wasn't as if he didn't deserve whatever Marcus chose to do with him.

Marcus ordered the doctors to find out how to unfreeze long-term cryofrozen people safely. He had to consider carefully which doctor to tell the whole truth to before settling on Dr. Marin. The doctor's medical curiosity knew no bounds and he wasn't inclined to excessive scruples. Just the man for this job.

Finally the cryotubes arrived and were safely settled in the smaller experimental hanger. Admiral Marcus stood at the door after the techs had left and just looked at them, a satisfied smile playing about his lips. Then he took out a copy of that badly-damaged photograph and began walking among the rows of cryotubes, peering through the mildly-frosted faceplates at each of them, his footsteps echoing in the quiet.

Men, women, even a few children. They were of every race, but all were so still and cold that he felt surrounded by corpses. He'd gotten through all but the last row, and still no Khan, unless that one at the beginning... but that one had had a vicious looking facial scar and a beard, so it didn't seem too likely.

Marcus was at the last-but-one cryotube when he found him. It was definitely the man in the picture, but Marcus found himself dubious that this was actually Khan. He looked so bloody young. This guy had really ruled a quarter of the Earth? Marcus shook his head. Well, they'd wake him and if he wasn't Khan or someone else suitable they'd put him back to sleep and wake the bearded man.

He called one of the techs back and told them to prep. that particular cryotube for revival, then went off to see how the plans for the Dreadnought vessel were progressing. Hopefully better than last time, or he might have to cancel the project. Dammit, they NEEDED Khan.

It wasn't until two days later that the doctors woke Khan, and Marcus was stuck in a Star Fleet meeting arguing with the other Admirals about the next year's budget. Pike in particular kept calling attention to the increases for Section 31 and demanding to know which projects the money was for.

"Yes Sir, I am aware that you can't give us details of exactly what Section 31 is working on, but an increase of this size needs some justification, especially when," and here Pike leaned forward to emphasize his point, "the money is already in use for training cadets. We need every new officer we can find after the Narada incident, as you well know."

"Just what do you want me to tell you, man? A lot of the money is for deciphering the Narada's systems and for improving our own, I can tell you that much. There is much we can learn from a ship from the 24th century, but we need the resources to study it."

"You're concentrating on weaponry, aren't you?"

"Chris, we lost Vulcan and we nearly lost Earth, dammit! To one vengeance-mad Romulan and a few friends armed with a fancy ship and weapons we'd never seen before. If we just sit here, exactly how long do you think it's going to take for the Klingons to take advantage, or the Romulans?" A couple of the other admirals nodded at this. The Narada had cost the Federation dearly. Too dearly.

Pike rubbed his forehead irritably. "I'm not suggesting we 'sit here', but taking money from the Academy when we're short-handed as it is is not the way. And why does all the development work have to be done under Section 31's mandate anyway? Surely there's a lot of it that could be done openly..."

Marcus suspected this was actually the crux of Pike's recent problems with him. They'd been friends once, and he'd even been the one to talk Chris into entering Starfleet in the first place. But the man was too stiff-necked and narrow-minded for his own good sometimes and they'd drifted apart once Marcus had been put in charge of Section 31.

By the time the meeting was over, Marcus had gotten most of what he wanted, minus a couple of projects being under the Science control rather than that of Section 31.

After the meeting finally ended Marcus entered his office, closed and locked the door before calling the Jupiter Section 31 base medical. It took them a few minutes to respond and Marcus grumbled, calling up a report on his PADD and fiddling with it. He'd just started brewing a cup of coffee when the screen cleared and Dr. Marin showed up, looking harassed and unhappy. "Admiral," he said.

"How goes the revival of our man from the past?" asked Marcus.

"There have been some complications..." said Marin, frowning. "He's unfrozen and we have him stabilized for now. It looks like the protocol used to freeze him was not the same as any of the examples we had available, and the different physiology only made things more difficult. He went into shock, then cardiac arrest and we've had to put him on a ventilator. He likely has brain damage, but we won't be able to tell how bad it is until he wakes up."

"The wrong protocol? Oh for the love of... just how bad is the brain damage likely to be?"

"We don't really know yet. It's a hypoxic-ischemic brain injury-"

"In Standard please," interrupted Marcus.

"His brain was deprived of oxygen and nutrients for long enough that there is likely diffuse damage to various areas of the brain."

"Will he live?"

"Yes, probably, but he could be restricted to a vegetative state or have less severe issues if he does come out of his coma."

_Great. Just bloody wonderful_, fumed Marcus, running a hand through his hair and standing up from his desk. After all this effort, to have Khan be damaged... assuming he survived at all. He should have had one of the children woken first to make sure the procedure worked before reviving Khan. They'd undoubtedly grow up to be monsters anyway so it wouldn't have mattered if they died.

It was nearly two weeks before Khan woke.

A/N: Obviously, Star Trek has a very different history than the real world, and cryopreservation, genetic engineering, and space flight advanced much more quickly there than they did in reality. I think people seriously underestimated just how hard these things are when they were writing Star Trek. I do have some knowledge of what's involved in genetic engineering, and that will leak into this story and how I portray the situations and people.

Many thanks to my reviewers. If you sign in I can give you an individual reply.


	3. Survival

**Chapter Two: Survival**

Khan stirred and opened his eyes a slit, then shut them and groaned. Too bright, it felt like someone was trying to shove a knive into his head. What was going on? Another failed assassination? He tried opening his eyes again, got the same result and kept them shut.

Then it was sound, like footsteps but loud, much too loud. Khan tried to roll over, hiding his face in the pillow, but found he couldn't make his left hand move. Hands touched him, confining, preventing him turning over, and loud, too loud voices said something he couldn't understand. Khan thrashed around frantically, then lay still.

He was obviously either injured or drugged, too much so to do anything useful. Best to lie still... He opened his mouth to ask them to turn down the lights but found himself groping for the right word. The lights stayed on and Khan stayed silent. He'd never felt so helpless before in his entire life. Eventually he fell asleep, dreaming of cages with iron bars and a spaceship roaring into the sky.

Khan spent much of the next two weeks drifting in and out of consciousness, being assaulted by light and sound whenever he was awake and struggling to communicate with his captors.

Admiral Marcus was most disappointed with his newest experiment and considered terminating him and waking a second Augment. Just to compound his frustration, they had got enough out of the man to determine that he was indeed Khan. What a stupid waste. Marin suggested that Khan could still be useful for research into Augment physiology and abilities even if he recovered no further. Marcus agreed, and turned Khan over to him.

For Khan, this time was hell. He could barely communicate at all, and while his captors had finally figured out the sensory issues he was having and provided sunglasses and earplugs, they certainly didn't seem to have any other compunctions about their treatment of him. One of their experiments resulted in broken bones.

It was fairly obvious they were trying to figure out what he could do, and their reactions confused him at first. It was as if they'd never seen an Augment before. It was that, along with a few comments, that led Khan to finally figure out that he had woken up well over 200 years in the future. Two hundred-plus years out of place, and utterly alone in the hands of enemies he knew nothing about. Oh joy. Maybe he should have stayed and fought till he was killed like so many others. It would have been better than this.

When Dr. Marin and the guards came to pick him up from his cell, he punched one guard in the nose, kicked the second, knocking him into the third, both of whom went sprawling on the floor. Khan had just launched himself at Dr. Marin when the flash-bang grenade went off. Suddenly blind, deaf and in agony, Khan screamed, landed badly on top of Dr. Marin and passed out. The guards dragged him back into his cell and left him there, lying on the concrete floor.

Some indeterminate time later someone Khan didn't remember seeing before showed up outside his cell, looking down at Khan where he was still sitting on the floor. Khan squinted up at the silhouette, regretting the loss of his sunglasses. "Khan," the man said, "I am Admiral Alexander Marcus. You are at my mercy. I also have your people, all of them, frozen in cryotubes. If you try anything stupid again I will kill them one by one in front of you. Do you understand?"

Khan considered pretending he didn't understand, but Marcus continued "Whether you understand or not, this is your only warning. You mess up again, they'll die." The Admiral turned and walked away without waiting for Khan's answer.

Eventually his luck began to change. Of all things, it began with a pad of paper and a pencil.

Khan was bored and very grumpy when Dr. Marin and his friends arrived that morning. "How are you feeling?" asked Dr. Marin, pointing a tricorder at him from about 4 feet away. The doctor was still using his left hand, Khan noted with amusement. Normal humans were so fragile.

Khan didn't bother replying, treating the doctor's fake concern with the contempt it deserved. He turned away to stare at the wall of his cell.

"Good, your red blood cell count is back up to normal. You should be feeling fine." Dr. Marin paused. "I know you can communicate better than this, so how about you at least say hello this morning," said Dr. Marin, getting a little exasperated. "You know, hello?"

Khan twitched, disliking the ridicule. "Say hello to... why?" said Khan. "Don't enjoy company you. Of yours," said Khan. He knew he'd mangled the wording, but it should at least get the meaning across.

"I suppose not," said Dr. Marin. "We'll be testing your lung capacity before and after exercise today, so there's nothing you should find too unpleasant."

Then it was off to the labs and breathing into the machines, running on a treadmill for half an hour, and breathing into the machines again. Khan didn't particularly mind that. It was nice to be able to stretch his legs. After that they wanted to draw his blood for some tests. Khan let them.

They seemed to be very interested in his blood. Granted it was good material for studying his genetics and it had a few unusual properties related to rapid healing, but why did they need so much? Next to him someone had put a notepad and pencil. Idly, he picked up the pencil and began to draw. First a caricature of Dr. Marin, then the Botany Bay.

One of the techs peered over his shoulder. "Hey, I didn't know you could draw," she said.

Khan rolled his eyes. Just because he had brain damage that didn't mean he'd lost every ability he'd ever had. "I had paper...not," said Khan.

"Yeah, I suppose it would be kind of hard to draw without pencil or paper. I'll ask Dr. Marin if you can keep it. You must be pretty bored in that cell."

Startled, Khan watched her leave. The medical staff usually seemed to think of him as an experimental subject rather than a person. She must be new here. He'd have to remember her face. Long black hair in a pony tail, medium height, dark skin tone but couldn't see her face. She vanished into another room.

He went back to drawing, and doodled a few relevant equations beside the Botany Bay's engines. Soon enough Dr. Marin came back to release Khan from the machine and take his blood to the refrigerator. Marin then turned to peer at what Khan was doing. "What's that?" Marin asked, pointing at a detailed cross-section of the Botany Bay.

"Botany Bay," said Khan.

"Nice work," said Marin. "Did you design the ship?"

"Yes," said Khan, not wanting to explain that while he'd done some of it, the bulk of the project had been overseen by Evan Tensing. Evan was probably safer asleep. He was certainly a lot happier than being a prisoner of these lunatics. And there was a possibility Khan's skills would get him an upgrade in status from 'guinea pig'.

"Interesting," said the doctor, nodding. "You may have the paper and pencil if I can have those sketches."

Khan handed over the sketches, and Dr. Marin smiled until he spotted the caricature of himself, at which he went rather red. Khan smirked. Normally he'd have been making the doctor miserable with sarcasm, but his speech issues made that impossible. This was a useful substitute, especially if Marin now had to show the caricature to Admiral Marcus.

"Ok, back to your cell Mr.", said the doctor and Khan allowed himself to be led back to his cell. Even if his captors didn't want to use his skills, at least he'd have something to do other than read old novels from his time and even earlier.

A/N: Kat, do you mean psycopathic rather than psychotic? If Marcus were psychotic, he ought to be hallucinating.


	4. A Promotion from Guinea Pig

The next morning Khan was perched on his bed drawing when he heard footsteps. He put down pad and pencil and waited.

Admiral Marcus appeared outside the transparent aluminum door, flanked by Dr. Marin and four guards. "Admiral," said Khan, getting up and walking closer to the door. A couple of the guards shifted uneasily at this.

"Khan," said Admiral Marcus. "Glad to see you're feeling better. Just how much experience do you have with engineering and weapons design?"

"Enough," said Khan. "old." So Marcus needed weapons... Humanity never changed much, did it? Khan wondered who Marcus was fighting, not that it really mattered. What mattered was getting him out of his cell and his crew out of those cryotubes. He'd get his vengeance on Marcus for treating him like an animal later.

"Good," said Marcus, smiling. "We can certainly get you up to speed. I'll send the relevant information to your PADD. I want you ready to do something useful by next week. If you do well with it, I may even let you out of this cell."

"Yes," said Khan, then realized he had a problem. What day was it? "Day...to. "

Admiral Marcus merely looked confused.

Khan tried again. "Day week?"

"Oh, today's wednesday. I want you up to speed next wednesday."

Khan nodded, internally cursing his difficulty with words. It was maddening, and it made him look weak.

Khan spent the next week reading and rereading the PADD. He discovered to his horror that he kept forgetting information, especially if it was stored in words. He drew everything he could as diagrams or rewrote it as equations. If there hadn't been so much riding on it he would have enjoyed the challenge of learning the changes in technology. Warp technology looked fantastic... if only he'd had it back in the '90s the Augments would have been ruling an intersteller empire by now!

Dr. Marin left Khan almost completely to his own devices, much to Khan's relief. That meant he wasn't wasting energy restraining himself from attacking the man. The broken wrist Khan had given him in his escape attempt wasn't nearly enough to pay for the man's behaviour. The man should have more sense than to cage and mistreat an Augment.

One week to the day, Admiral Marcus returned and quizzed him on what he'd learned. Khan could tell he was pleased with the results, even if he had to answer some questions by drawing them or using mathematical equations and a few just plain weren't answerable without better language skills than he had.

"Well done," Marcus said finally.

Khan waited for him to continue.

"There is a ship that is a pet project of mine. It will need to be bigger, faster and better armed than anything we currently have..." Admiral Marcus began to explain the Dreadnought project.

Khan nodded as the Admiral explained what he was trying to do. It certainly sounded like an interesting project. Evan would have loved it. Not that putting something like that in the hands of Admiral Marcus seemed like the best of ideas, but that really wasn't something he had much choice about for now.

"I'll send you the details here for now, but if you produce something interesting I might give you more freedom. IF I do, you'll have to be under another name, of course."

"Free family," said Khan. A false name? If it got him and the others free he'd even forget about taking vengeance on this fool.

"Your family? Oh, you mean the Botany Bay's crew."

Khan nodded.

"I'll think about it. You'll have to do a lot to earn that."

Khan stared at him, wondering how far he could trust him.

"I can't just release all of you into earth's population. You'd stick out like sore thumbs and it would be my head on a pike if anyone found out, let alone if one of your lot hurt anyone. No, you'd need to leave federation space entirely."

"Botany Bay try."

"Yes, you did, I suppose." Admiral Marcus fell silent. "Very well. If you do everything I ask, produce the weapons I need and help me win the war against the Klingon empire, I will provide you and your crew with a ship at the edge of Federation space and you will take it and never return."

Khan smiled, one which actually reached his eyes. "You do... this, I design weapons."

"Yes."

Khan nodded.

"Welcome aboard, Agent John Harrison," said Admiral Marcus. They both smiled.

Khan spent the next three weeks going over the systems suggested for the Dreadnought class and trying to fix problems or find improvements. At least, that was the main thing he was doing.

They actually got him to see a speech therapist, although he only seemed to be making limited progress. It was still vastly better than when he'd woken up and she seemed to think it might keep improving with time. Given his augmented healing abilities, Khan thought she was probably right. Still, Khan found himself thinking forward to when he would see his people again, and dreading their reaction to the changes in him. It would still be worth it just to see them again and to get out of here.

He also had to get used to answering to 'John' or 'Agent Harrison' and learn how to behave as a member of Section 31. 'John Harrison' was a Section 31 agent who'd recieved a brain injury on a mission and turned to his other specialty, weapons design. He would still have to put up with a guard/watcher/handler, with the explanation that his injuries meant that he needed extra oversight, but his abilities were too valuable to go unused.

Overall, Section 31 seemed operate in a similar manner to how intelligence agencies operated in his day. He couldn't really say much about specifics seeing that he'd never been part of one before.

One interesting thing he learned was that much of what he'd seen so far and had experienced would be considered both illegal and immoral by the rest of society. Interesting, and something it might be very useful to remember if Admiral Marcus played him false.


	5. Agent John Harrison

He had a couple of conversations via PADD with what would be his new team leader, a Dr. Maria Shostakovitch. He'd also been given a different design of PADD with a larger screen on which he could draw with a stylus. That was going to be immensely useful.

There had also been some fine-tuning of the glasses so that light didn't leak in round the edges. They looked a little odd, more like goggles than sunglasses, but they meant he could finally handle normal indoor lighting without getting a headache. That was worth a lot. Finally, it was time to go and meet the rest of the team. They were currently based in London, so that meant spaceflight.

He'd been surprised and a bit embarrassed to learn that he wasn't on earth already, but on a space station near Jupiter. How in the world had he failed to notice that? But between the artificial gravity, the lack of windows and the state he was in when he woke perhaps it wasn't surprising. He was rather looking forward to the trip. The last time he'd been voyaging through space he'd been cryofrozen and unable to enjoy it.

His minder, Connor Hathaway arrived outside the cell and unlocked the clear door, swinging it wide. "Everything ready?" Connor asked.

"Yes," said Khan. Khan slung the single duffel bag containing his PADD, clothes and a few odds and ends over one shoulder, and left the cell for the last time. Good riddance to THAT!

They wound their way through the rest of Section 31 station, going from the medical labs through one of the hangers and the living quarters for the staff before arriving at the docking bay.

The takeoff was very uneventful, given that they were leaving a space station and weren't fighting a planet's gravity to get away. The view outside, however... Jupiter loomed vast and aweful in the distance, the space station like an intricate piece of wirework diminishing as they travelled away. Moons, bright and shining across a black field sprinkled with more stars than he had ever seen before in his life.

Khan leaned towards the window around Connor. Khan's fingers itched for his sketchbook even though he knew perfectly well that even paint would never capture it fully. How Connor could remain oblivious to something so beautiful... ah well, it was his loss.

Eventually Khan became tired of staring out the window and rummaged through his carry-on for his PADD. He might as well do some work while he was here.

"You haven't been in space much, have you?" said a brown-haired woman on the other side of him, smiling.

"Just not seen... Jupiter in a while," said Khan, remembering that John Harrison had seen many different planets and star systems. For a moment, Khan felt an odd jealousy of his invented persona.

"It is a nice view," she agreed. "Where are you off to?"

"Kelvin," said Khan.

The woman looked confused.

"Kelvin Memorial Archives," said Connor from beside him.

"Oh," she said, sounding a little disappointed, that's nice. "I'm heading out-system."

She obviously hadn't the faintest clue as to who or what he really was. It was nice to deal with someone who didn't think of him as a dangerous animal, even if it was all based on lies. He missed his family!

Once they reached earth, they transferred at the San Francisco Spaceport beside Starfleet Headquarters. That was going well enough - the complexities of light and sound were confusing even with the glasses and earplugs, but he just followed Connor. Then there was a tremendous crash just behind him.

Instinct took over. Khan dived to the floor and rolled behind a family of Andorians with a very large luggage cart, grabbing for his sidearm with one hand. It wasn't there, of course. Khan peered around the Andorian family's cart to see an overturned trolley cart with a box of spilled communicators along with a lot of people staring at either him or the cart.

Connor hurried over and grabbed Khan by the arm, mouthing words Khan couldn't hear over the ringing in his head but that looked like 'calm down'. Embarrassed, Khan stood up and dusted his knees off. He allowed Connor to continue leading him towards the terminal for the London shuttle.

The rest of the journey was uneventful.

The Section 31 base hidden by the Kelvin Memorial Archives was only moderately well hidden. Khan sniffed.

They stepped through a door marked "Staff Only", and were greeted by a hatchet-faced woman who checked their ID's before waving them through. The base itself was a plain battleship grey, and contained many long corridors. Khan's headache had never really gone away and he was beginning to wish they would just reach his quarters so he could lie down.

Of course, that was when he ran into a couple of his new teammates, the leader Dr. Maria Shostakovitch and a Dr. Carol Marcus. They were both rather short for Normals, and Khan found himself looking down a good long way. He was interested to note that if Carol was related to Admiral Marcus she didn't look much like him. Pixie cute and very young, with white-blond hair, blue eyes and long legs, she looked more like a model than a doctor of physics. Never mind, appearances were presumably deceptive in this case.

They both wanted to talk shop at once and called over some of the other teammembers. When Maria commed a Temujin Genghis and told him to 'come over here and meet the newbie' Khan nearly did a double-take. Was someone playing a practical joke? But no one else seemed to notice anything unusual. Perhaps the man's parents had merely had an appalling sense of humor.

Khan was about to let himself be dragged of to look at the newest set of diagrams and some computer models of the warp engines despite his pounding head when his pain levels abruptly surged and his vision went black. Khan staggered. Connor yelled as Khan fell down, feeling someone try to catch him on the way.

A lot of blurred confusion later and he was in Sickbay with far too many people fussing at him. He finally got Connor to tell him what had happened. Some idiot had taken a flash photograph. Undone by a trifling photograph, of all things! Khan buried his face in his hands and wished the world would just go away.

They let him go after a couple of hours, instructing him to get some rest and take it easy for the next day or so - as well as to avoid bright lights and loud sounds, as if Khan hadn't figured that out the day he woke up.

He was glad to finally reach his quarters and close the door on the world, even if it turned out he was stuck sharing a bathroom with Connor, who was in the bedroom next to his.

A/N: Can anyone tell me where the names of Khan's coworkers are from? My brain apparently decided this story needed bad puns and strange references.


	6. Engines and Ear Protectors

At breakfast the next morning, Khan got properly introduced to the team. Temujin Ghengis, who turned out to be the one responsible for the flash, apologized profusely. "Don't do again," said Khan.

"It won't happen again," Temujin said earnestly.

Khan nodded and smiled, and Temujin finally seemed to relax.

"Your name," said Khan. "As Ghengis Khan?"

"Oh yes, my mother studied central asian history in university, and then she met my dad. His last name's Ghengis and they couldn't resist."

"Parents," said Khan. Everyone laughed, though Khan was laughing for a slightly different reason. Between him and Temujin, they had the full set, and no one but him even knew.

"Hi, I'm Al Macgregor," the last team member said. "I've been working mainly on the subspace engines and the warp drive."

Khan nodded and smiled. "Warp drive... fun." said Khan. Not quite what he'd meant, but hopefully close enough.

Temujin laughed, as did Carol. "Don't let Al get started on warp equations. He can do them in his head and he'll go on about how beautiful they are for hours," she said. "Personally, I'm more interested in figuring out how to adapt the Narada's laser cannon so that the power required doesn't draw down the warp core too far and drain the available power for shielding ..."

Khan was glad he'd brought his PADD to breakfast. He had a feeling he was going to need it.

The next week was a steep learning curve even for Khan, but between his PADD, and a lot of hard work and extreme stubbornness he thought he was making enough progress to satisy Admiral Marcus. He'd even been useful, persuading Carol and Maria that a gun that jammed in muddy conditions, sandy conditions and very cold conditions while overheating and exploding when too hot was worse than useless to a force like Starfleet that might have to fight in any combination of these conditions without prior notice. That alone had probably saved a good many lives.

Khan shook his head. None of the others had any combat experience worth mentioning, and the lack of field experience showed. No wonder Admiral Marcus had wanted his input. He was trying to prepare for war in a time without true warriors. That, Khan could help with.

Gradually, the engine designs became more complete. He'd gotten to know the others a bit better by this point, and was beginning to feel more at home. Temujin with his photography obsession, Carol's ornery and ancient cat, Maria's dry sense of humor and Al's engines.

He had to remind himself that they were not his people and would turn on him instantly if they knew what he really was. There was no sense in getting too close to those he could never trust. It would only burn him in the end.

One day they were testing a new sublight engine prototype for small craft. Khan wondered if he should absent himself from this entirely or if standing in the doorway at the far end of the room would be enough. It was only a very small engine, after all. He hesitated, feeling ridiculous. Carol looked up from rummaging through her handbag and said "Catch", throwing him a pair of pink fuzzy ear protectors. Khan frowned at them. No way was he wearing them.

"Don't be silly, put them on," said Carol. "Or do you like being in agony?"

Khan put them on, wondering who had designed the hideous things in the first place. "Thanks," he said. "No photo!" he said, spotting Temujin bringing up his camera.

"But it's perfect," complained Temujin. "Just one. You know I don't use flash around you anymore."

"Boys, stop it," said Maria. "Temujin, no pictures, and Khan, you'll wear the extra ear protection and stand by the door. You should probably get your own if you don't like the color." Temujin mock-pouted and put the camera down. The test located a couple of bugs, but nothing that Al wouldn't have sorted out in the next couple of days. Sometimes it seemed the technical problems were less difficult than the people ones.

The next five months went relatively smoothly.

The base at London wasn't that big, and he soon found himself recognised and greeted by most of the people there. The Section 31 people tended to socialize together as well as work together.

This rapidly became awkward, because he wasn't allowed to leave the base even with Connor in tow, and he couldn't easily explain that to people. Most he could bow out of gracefully with reference to the eye and ear issues, much as he hated showing weakness. Honestly, did Al think before asking if he wanted to go to that rock concert? But other things were harder to say no to.

"John, do you want to go rollerblading in the park after dark tonight? Temujin, Alexa and I are going so far."

Khan winced internally. He'd like to go. He was sick and tired of the base and he'd love to get out, but he could see Connor glowering at him from the other end of the room. "I really need to do... work tonight."

"Ok," said Carol, looking a little confused, almost hurt. He couldn't blame her, since it wasn't as if he did much round here but work. She probably thought he didn't like her, or that he still carried a grudge against Temujin for the mishap the first day. That just wasn't right. He'd hand the problem to Connor and see how he handled it.

She turned to leave the room. "Not supposed leave," said Khan.

"What?" said Carol, turning back. ''You aren't allowed to leave the base? Why?"

Conner glared at Khan, abruptly striding up to join them. "John has PTSD from the Incident as well as a high level of combat training, and Command would rather he didn't cause any incidents with civilians. It's safer that he stays here."

"Why didn't you say something about that earlier?" Carol demanded.

Khan looked away as his jailors replaced one lie with a half-truth. He'd suspected that his captors would have several levels of explanations if needed, and this confirmed his guess. Now he had another infirmity paraded in front of the world - this time one that wasn't even his. Just wonderful. On the other hand he might be able to use that somehow later...

"I'm sorry. But there is nothing to be embarrassed about," Carol said. "Since you can't leave, is there anything I can get you from off base?"

After that the word went round his colleagues and people stopped asking. He couldn't help but feel a bit left out. The place had a gym but he couldn't stretch himself to anywhere near his actual limits or he'd blow his cover and Admiral Marcus would be furious.

On the bright side, his language issues were now a lot better than they had been, even if his grammar was highly... inventive. Khan spent a lot of time on the computers, trying to get a better handle on the society he'd landed in, and learning the ins and outs of their computer equipment while he was at it.

Admiral Marcus popped in and out at unexpected intervals, checking on their work and stopping to chat with Carol, who was indeed his daughter. Admiral Marcus seemed pleased, and actually complimented Khan on his work a couple of times. The second time this happened, Khan dared bring up his people. "Can I see family?" Khan asked.

"They won't look any different than they did the last time," said the Admiral.

"Still sleep?"

"Yes, John, they do that a lot."

Khan glared at him. While Admiral Marcus might find his insistance amusing, it wasn't funny for him. If he ever found out Marcus was lying to him the Admiral would find he was playing with deadly fire indeed.

"Still want see them."

"You know I can't let you do that."

"Why? I do what you want."

"They're safe. In a safe, hidden place that I do not let anyone know of. That includes you." The Admiral sighed.

Khan was almost certain that place was on the Jupiter base, but that certainly didn't match seeing them with his own eyes and knowing for certain where they were. Khan didn't like the situation. He was being forced to take an awful lot on trust, and Admiral Marcus was the one getting the benefit from their deal so far. What was to keep him from reneging on his word once he had what he wanted?

It was time for Khan to put some of those computer skills to use and see what he could discover for himself.

But before he had a chance to do more than disable his computer's logger and discern that a shipment far too large to contain only his cryopod had arrived at the Jupiter base at the correct time, it was time to move back to the Jupiter base, and actually build some of those projects they'd been working on.

Khan smiled despite himself. That dreadnought was going to be quite something to see when it was built. He'd already nicknamed it the Vengeance inside his head. Hopefully he wouldn't need to take vengeance of another kind.

A/N: Kudos to Cmdr's Monkey for figuring out that Temujin is Ghengis Khan's birth name. As for Shostakovich, Dmitri Shostakovich was a 20th century Russian composer.


	7. Betrayal

Once on the Jupiter base, he got handed a demand from the Admiral to create a better torpedo. Marcus wanted a whole bunch of things from the new weapon, some of which looked likely to be mutually exclusive. Lovely. He might be a genius, but that didn't mean he could change the laws of physics. This would likely keep him too busy to hack the computer system much.

It did, for the mucn of the next few months. Then something happened that changed his priorities. Khan was sitting in the almost empty mess hall late one night, having finally figured out how to make a torpedo engine that wouldn't leave a trail that would show up on sensors, when he overheard something from the two medical staffers eating at a table near the other end of the hall. "Oh, Joachim's way ahead of schedule. Significantly faster growth, language aquistion and so on. Sounds like a mini-professor some of the time."

Joachim? Khan tensed. Surely not... surely Marcus wouldn't break his word so obviously, and for so little benefit. Studying him was one thing, but if they'd harmed Joaquin and Suzette's three year old son, death would be too good for Marcus and the two people at the other end of the hall. Beside him, Connor picked at his food, obviously both exhausted and oblivious to what was going on in the room.

"When he isn't imitating Kelly's cussing," the other said. "God, the kid's cute." She chuckled quietly.

"Better you than me. What happens when he grows up and turns on you, or when the Admiral decides he's learned all he needs from the kid?"

"We're raising him right. Jo'll think of himself as one of us and be a real asset to humanity. He's too little to really remember the others much."

Khan's eyes narrowed as he pretended to study his plate. Not if he had anything to say about it, the boy wouldn't. Joaquin and Suzette would never forgive him. Khan abruptly realized that the fork had bent in his grip. Khan closed his eyes and counted to 10, then opened them and carefully straightened the fork. He couldn't let his rage get the better of him or he would get all his people killed. And he needed to listen.

But the conversation had moved on to other topics, leaving Khan fuming impotently and without any further interest in his dinner, or in sleep for that manner.

He glanced at Connor. The man was obviously exhausted. Khan almost pitied him. If the Admiral really wanted to keep tabs on him he should have assigned more than one person to do it. Oh well. Connor was quite welcome to go sleep if he wanted to, but he needed to spend some quality time with a punching bag.

Then he needed to get serious about cracking the computer system and finding out just what was happening with Joachim. It might not look like Jo was in any immediate danger, but he needed to know that for certain.

As for his agreement with Admiral Marcus, that could go hang. The man was patently lying to him._

Khan didn't get much sleep for the next while, though he allayed suspicion on Connor's part by doing much of his research in his room after Connor had gone to bed. With the changes he'd made to the logger, Khan was safe so long as no one saw his computer screen. Khan smiled, but it wasn't a kind smile. Connor should know better than to try to keep up with an Augment.

Unfortunately, getting the crew out didn't look like it was going to be easy. He'd located all of them, secluded in two different storerooms on Jupiter station.

Joachim, meanwhile, was living with Amy and Kelly Greenwood, two Section 31 people who lived on the far side of the station near the medical research labs. That area had its own mess and recreation facilities, which explained why he hadn't run into little Jo in the halls. It was tempting to go take a walk down that way, but he couldn't risk it.

Amelia he'd seen in the main mess hall during that overheard conversation, while Kelly was one of the doctors who'd been involved in the experimentation on him. Kelly likely knew Khan's real identity, but he wasn't so sure about Amelia. If she did know about him, she wasn't very observant.

That was all well and good, but how was he to get his people out when they were in three different places, well, four if he counted himself, and he was the only adult awake? Not good.

Khan also found out more about what Admiral Marcus planned to do in the event that Khan turned on him. There were orders for if something happened to Marcus himself - a deadman switch that meant all the Augments would die. That turned Khan's blood cold because it not only meant their deaths if he killed Marcus, it also meant their deaths if Marcus died for other reasons, which could be anything from a preemptive strike by the Klingons to a heart attack. Bastard.

There was nothing written down about giving the Augments their own ship and letting them go in the event of everything going right. Likely the man had been lying to him all along, using his desperation to keep his people alive against him. Vengeance against the conniving liar was definitely ON, but more important was getting his people out alive.

Khan pondered how to do this as he continued working on designing the torpedoes. What he had down so far would satisfy most of the Admiral's conditions, but not all, not yet. They were also getting rather larger than he'd initially intended. Certain shapes just didn't fit together and left a space... Khan concentrated on the torpedoes and tried to ignore his people's situation for now. Then something clicked.

If he moved one component only slightly, a cryotube could fit inside. He could explain the gap as access to the torpedo's interior, at least until he put the cryotubes inside.

Cryotubes from storage into torpedoes, torpedoes onto Vengeance, steal Jo from his minders and go. He'd have to do some work to make the Vengeance at least marginally operable by one man if this was to work. It would be difficult, but it would be possible. Khan smiled. He had a plan.


	8. Plots and Counterplots

Turning that plan into reality turned out to be a right pain. The biggest problem: how was Khan to get the cryotubes from storage into the torpedoes without someone noticing? It wasn't as if he could just roll them down the corridors.

And people were noticing his preoccupation. Not just Connor, who was getting exhausted trying to keep up with him; Carol kept giving him odd looks and twice asked him outright what was wrong. The second time happened in the mess early in the morning. It was really awkward...

"John, you're spacing out again. Are you sure you're alright?"

"Oh... Fine. Just thinking torpedoes."

"I think you got the hardest project of the lot of us. You sure you wouldn't like me or Al to take a look? Sometimes a fresh mind can see something useful."

"No. I'm ok. It's just taking time."

Carol smiled at him, but there was a brittle edge to it. "You're working way too hard. Seriously, do you ever sleep?"

"Not often enough," muttered Connor.

"Sleep little always," said Khan. It was even true. Augments often found they needed less sleep than Normals.

"I hate to remind you, but you suffered a severe brain injury not that long ago. You need to sleep." Her eyes sought Connor's, glaring as if to say _You're supposed to look after him, why can't you make him sleep?_

Khan glared back. He was quite capable of looking after himself! Though she was right that he would probably benefit from more sleep. But with his people in danger he didn't have much choice.

"She's right, you know," said Connor. "You're wearing me to a nubbin and I'm healthy. The Admiral won't expect you to work yourself to death."

_Oh wouldn't he?_ thought Khan bitterly. So long as Admiral Marcus got what he wanted he very much doubted Marcus would care if he died. In fact, he'd probably be pleased.

"Is that the problem?" asked Carol. "Look, my father may be demanding but he's not crazy and he knows you're still recovering. I'll talk to him for you."

Khan's eyes widened. Oh no! Bringing this to the Admiral's attention was the last thing he needed.

"No. Try to get more sleep," said Khan. "You right. I working too hard."

"It's no problem," said Carol.

"Thanks," Khan paused, then shrugged, deciding that having it reported that he was overworking to the Admiral probably wasn't such a terrible thing and too much protest would start to look suspicious all by itself.

Carol shook her head. John was too proud and stubborn for his own good. Why couldn't he just smile and accept help when offered? Men. But she was definitely going to be bothering her father about this. It wasn't just about how he was overworking.

There was something about John and Connor that didn't add up. It was almost as if John felt himself a prisoner and didn't dare trust anyone. Connor's behaviour didn't quite fit the role she thought he was supposed to be playing, either. Was there more going on than she'd been told? Dad did love his secrets, but she had a bad feeling about this one.

It took her a couple of days to actually get hold of her father, as he was heavily embroiled in assorted meetings in London and San Francisco.

She finally managed to catch him in his office before she started work. "Carol!" he said smiling. "What a nice surprise to hear from you. You should call more often."

"You are a little hard to get hold of, you know," she answered.

"Comes with the job."

Carol nodded. She knew that. She always had, considering that it had often meant she and her mother didn't see him for months at a time when she was growing up. Welcome to Starfleet.

They exchanged small talk and news of what she'd been up to for a couple of minutes, when Carol brought up what she really wanted to talk about. "I'm a bit worried about John."

"Which John?" asked her father, frowning.

"Agent John Harrison, attached to our group. He's overworking and he won't stop."

"Isn't that something Dr. Schostakovitch should be dealing with?"

"He's doing it because he's scared of disappointing you, so I don't think Maria would be much help. He's not healed and I know Connor's worried he'll make himself ill. Can't you tell him not to hurt himself and to back off a bit?"

"Did Harrison tell you that?"

"No, but he didn't deny it when I accused him outright. He didn't want me telling you at first. I think he's scared of looking weak, which is stupid. Most people hurt this badly wouldn't be trying to work at all, let alone on something like this."

Her father sighed, wearing a rather put-upon expression. "Carol, I really wish you wouldn't go adopting every wounded creature you find. He's not a tribble or stray kitten."

"I know that, Dad! And I was eight." Carol said, crossing her arms and frowning back at him.

"Harrison," said her father, "is bloody dangerous, and I'd prefer it if you didn't get too close to him."

Carol pursed her lips. So Connor was as much jailor as protector. Just what was going on here? "Apart from the pairing of advanced combat abilities and PTSD, dangerous how?"

"PT.. Isn't that a dangerous enough combination?"

"He hasn't done anything untoward the entire time he's been here except overwork himself and run Connor ragged following him around. He didn't even leave the base when we were in London."

"I should hope not, he isn't civilian-safe."

"Is he a prisoner then? Because you're treating him like one, rather than as someone injured in Starfleet's service. I swear he's afraid of you!"

"Look... sweetheart, sometimes the world isn't a pretty place. If you want to be in Section 31, you're going to have to get used to it. We've got war heading our way and I need to use every asset we've got to make sure we win. And sometimes we don't have time to treat them as nicely as we'd like. Do you really think Harrison would rather be stuck recuperating in some mental hospital? He'd go out of his mind with boredom and we'd be down a fine weapons designer."

"I'm not arguing with him being here, I just think its counterproductive to push him so hard he breaks. And don't call me sweetheart."

"What's he doing that's got you so worried?"

"Working constantly and not sleeping or taking any time off. He never smiles any more, either and he's been downright moody lately."

"Go bother medical or Dr. Schostakovitch. He's not your responsibility. If you must know, the man's always been able to operate with very little sleep and his being very focussed is normal."

Carol sighed. She clearly wasn't going to get any more information just now. If she wanted to know anything more she'd have to do some digging on her own. "Ok Dad." They spoke for a few more minutes and then ended the call.

Carol sat down and brushed her hair back from her face, thinking. The sensible thing would be to do as her father suggested and leave the situation to him. There was clearly something classified going on here that she wasn't cleared to know about. Not exactly unexpected in Section 31! If she poked her nose into everything that seemed odd around here she'd never get any work done and would probably end up in jail for espionage.

But her father had a habit of putting his plans in front of people's needs. Often that was exactly what the head of Starfleet needed to do. She would never have joined Section 31 if she hadn't agreed with his overall aims.

But it was also what had driven her parents apart. People got hurt in his plans, often including people who were merely in the way. She'd rather John didn't get broken as a side-effect of one of her father's plans. The man had lost enough already. She would definitely keep an eye on the situation - but for now it was time to go do the work she was paid for.

* * *

Admiral Marcus cursed after the call was over. Of all the people for his daughter to take a liking to, it had to be him. Briefly, he considered moving her to another project, but moving either her or Khan would slow the work considerably.

He hadn't wanted to bring Carol into Section 31 in the first place, but her skills really were needed there. Unfortunately the girl's heart wasn't so suited. She'd have been better off in some other part of Starfleet.

He'd warn Khan that he wasn't to lay a finger on Carol. Uneasily he recalled that one of the Augments' weapons had always been their charisma.


	9. Everything Goes Pear-Shaped

The next few months dragged on as the Vengeance continued to grow closer to their designs. It was beautiful, Khan thought. Sleek, powerful, big and dark where the typical Starfleet vessel was pale. It stood out a lot less visually against the darkness of space, which would be all to the good in action, but the color also amused him. Between the color and the name, the ship seemed decidedly sinister. As the lynchpin of Marcus' plans to start and fight a preventive war, that was highly appropriate.

In order to get the cryotubes into the torpedoes, Khan had eventually decided to make use of Scotty's transwarp equation and a miniaturized transporter. He'd never get hold of one of those officially - he'd have to steal one. He could crack the code needed to get in just fine, but he'd have to make sure nobody saw him with it. At least they weren't all that recognisable, looking more like a briefcase than anything else.

He was going to have to make Connor sleep because he would definitely figure out something was wrong. He'd explain it as the man having a cold if he had to, or even just say he was exhausted and Khan hadn't wanted to wake him.

Khan pushed his sunglasses back up his nose. There was a lot that could go wrong with the plan, and once he began moving his crew there was no easy way to explain the situation away. If everything went completely to hell he might be best off escaping and bringing the situation to the attention of the media and the rest of the federation. Non-humans would probably be best as they would have no prior experience with the Augments and no reason to hate them.

The best choice might be the Vulcans, as they had very recent experience as victims of genocide themselves. They were also on average physically stronger and smarter than humans, and therefore likely to feel less threatened by the Augments.

Yes, a good choice. With their nonviolent tendencies and the recent violence against them, they might even like to have the Augments present on New Vulcan as a form of protection. The higher gravity and dry climate was more suited to Vulcans than humans but was within easy Augment tolerance... but he was getting ahead of himself here.

New Vulcan was well out of torpedo range from Earth, so he couldn't just launch the torpedos there broadcasting an explanation as they went. He'd need to take them there in the Vengeance. Not good; there would be people on the Vengeance and he didn't really want to kidnap his coworkers. They'd try and stop him and it would be distracting when he was trying to fly the ship. Maybe early in the morning before most people were awake...

He'd also need to grab Joachim before doing any pleading for his people's lives. The boy would be far too vulnerable in Marcus' hands. Jo would also be much easier for people to sympathize with than an ex-dictator.

The boy would probably be in daycare if he left in the morning... he'd have to check his carer's hours.

Khan continued fiddling with the torpedoes as he plotted.

* * *

Several months on, everything was ready. The Vengeance was flyable but not fully finished, the torpedoes had been loaded onto her and Khan had the codes to get to the miniature transporters. Maria really ought to have hid it better when she keyed it in last week. Incompetent. He'd also cobbled together an extra powersource that should allow multiple warps without recharging.

That morning, Khan was tense. He picked the lock on Connor's door, walked in and shook the man's shoulder. No response, and the water glass by the man's bed was empty. Khan smiled. Good, what he'd given the man should make him sleep the day away. He walked out, closing the door softly behind him.

Next, the miniature transporters. That was near the other end of the base. He wound his way through the corridors, stopping briefly in the mess to grab coffee and a muffin and continue on his way.

The halls were quiet this early. Khan keyed in the code to the room containing the 'special' supplies. The door whooshed open and Khan walked in unopposed. Next, the locker with the miniature transporters. That was even easier to get into, and Khan picked up two of the transporters, carefully signing it out under Maria's name.

Stage one, accomplished. Next, Khan went to the Vengeance. There were a few more people here, and the risk correspondingly higher. Khan nodded pleasantly to Al as he walked into the Vengeance's main hanger, then on to the first torpedo where he'd left the external power source.

He crouched beside the torpedo and carefully plugged in the power sources to the transporters. They were a little odd-looking since he'd cobbled them together out of spare parts, but it should work just fine. Then he opened the torpedo and set the coordinates. Yellow light shimmered as the cryotube appeared. Khan peered in the faceplate. Hiroko Sen lay there, quiet and cold, waiting to be woken. Khan smiled at her and closed the torpedo back up.

Then it was on to the next, and after that the next. One by one the torpedoes filled with Khan's crew. Khan was four torpedoes from the end when Carol Marcus poked her head round the side of the torpedo. "John, what are you doing?" she asked.

Khan froze, then forced himself to smile and relax. Of all the people he didn't want to see right now... "Just making a few final adjustments," he said. Behind her two more sets of footsteps.

"With a miniature transporter?" said Maria. "That doesn't make sense. You don't have permission to access those. How did you get at them?"

"Where's Connor?" asked Carol.

Maria reached for her communicator button.

Khan hit her in the neck with one hand.

Al shot him with a phaser. It was set to stun, and Al didn't have time to regret that as Khan attacked him. Carol hit the fire alarm, and that began ringing and the sprinklers started spraying everything with water. Ow! his ears. Damn.

Carol looked at John. "Why?" she said. Silly girl didn't even have a phaser on her.

"Your father holds my family hostage," said Khan, and stunned her with Al's phaser.

Khan carefully pushed the three of them under the torpedo. He took their communicators and stunned Al and Maria with the phaser to make sure neither didn't woke up too soon. He didn't particularly want to kill them, but if it happened, it happened. The phaser beeped. Khan cursed. The stupid thing was low on power. Looked like Al hadn't kept it fully charged. He tossed it aside.

Khan ran down the ramp, holding the transporter in one hand with the attached powersource flailing along behind it.

"You ok there?" asked Katya. Khan couldn't really hear her over the ringing in his head, but risked an answer.

"Fire near torpedoes. We need evacuate... here." said Khan, gesturing madly at the docking area. The longer he could keep worried firefighters from entering the vessel, the better.

"Oh great," said Katya from behind him. "John, stop!" We need more information..." But Khan wasn't paying attention. He got a lot of startled glances as he ran through the halls, but only a couple of people tried to stop him and he simply brushed past, knocking them aside as he went and leaving them staring after him. Speed was now far more important than secrecy. Curse Carol's quick thinking!

It took only a couple of minutes for him to arrive at the daycare. Khan opened the unlocked door and glanced around at the group of toddlers, small children and two adults who were staring back at him.

With a squeal, a small blond blur launched himself at Khan's legs, yelling "Uncle Khan, uncle Khan!" knocking down the multicolored block tower that had been teetering on the table. One of the toddlers began to bawl.

Khan started entering the data for transport back to the Vengeance, his fingers flying over the keys, saying "Yes, Joachim, it me. Hang on!" With a yellow shimmer, they transported back to the main hanger bay on the Vengeance.

Right into the middle of a group of 10 heavily-armed firefighters cum security, in hazmat suits.

Khan launched himself at the nearest, intending to grab the heavy-duty phaser he was holding. He tripped over Jo, who was still holding onto Khan's legs.

Jo shrieked and let go, Khan rolled forward into an upright position and grabbed the phaser, breaking the man's wrist as he went. Just in time to be shot in the shoulder by one of the others, with a phaser that definitely wasn't set to stun. He managed to hang on to the phaser, but there was no way he'd be able to shoot accurately for the next few minutes. So he used it to blungeon nearby guards instead.

"Jo, hide!" yelled Khan, barely registering the child as he ducked behind a torpedo.

The next 5 seconds passed in a blur. Khan downed the last guard and looked up just in time to see another group entering the hanger. Khan felt a burning sensation and look down. Apparently the shoulder wasn't the only place he'd been shot. There was no way he was going to win this and get the Vengeance out of here now. Khan wavered on his feet, then dived for the remaining transporter.

"Put the weapon down!" yelled the soldiers.

"Jo come," yelled Khan, beckoning. The child ran to him, but had tears on his face. Khan grabbed his arm and stabbed the preset location button. He felt himself hit again as they disappeared.


	10. To Plead for Mercy

They landed on the steps of the main square in Starfleet Headquarters. It was dark. Khan tried to stand up, but everything tilted and he found himself on the ground again. Not good. He wasn't going to be able to get to the Vulcan embassy in this state. He looked at Jo. No, he couldn't expect the kid to find it on his own with no map and then explain to the Vulcans what was going on.

He was going to have to do the unthinkable. Be as public as possible and hope the whole mess couldn't be hushed up by Admiral Marcus. He looked around. Unfortunately, it was night and there was nobody close. Damn. Where were the media when you actually wanted them? Fickle bunch of parasites.

"Uncle Khan, you're hurt," said Jo. "Uncle, are you listening?"

"Yes," said Khan, and coughed, tasting blood. "Vulcan... Embas..."

Jo frowned, then his face lit up. "I'll go get help," he said. "You wait. I'll be back soon, I promise." He then ran off across the square towards three people standing talking at the far side of the square. Khan reached up, and managed to get his sunglasses off on the second try. He still couldn't really see details, but one had a cane, and he suspected all were Starfleet from the shape of their silhouettes.

Not ideal at all. Khan watched as Jo ran up to three men and they turned towards him. Khan pulled out his earplugs and listened, but it was too far away for him to hear anything clearly. He settled down to wait, and examined his phaser burns. As he thought, they wouldn't be fatal provided he didn't lie out here in the cold all night. No doubt whoever Jo brought back would freak out at how bad they looked and insist he got immediate medical attention. That would be nice. They hurt.

Khan closed his eyes and rested his head on the step, then opened them. He couldn't pass out - he had to be able to talk to them! Meanwhile...

* * *

Admiral Pike and the former Captain Kirk walked somewhat erraticly through the square on the way home from the bar.

"Admiral, Captain," said a familiar voice just ahead.

"Spock!" said Kirk. "Found your new Captain yet, you reprobate?"

"No. I was concerned about your state of mind," said Spock. "Yet you appear well enough, if a little intoxicated."

"Yeah, well, you know me."

Pike turned, seeing movement. A human boy, maybe four or so, running up to them. "Sir, uncle Khan is hurt. Please help!"

"Ok. Where is your uncle?" said Pike.

"Vulcan. Are you Vulcan?" said the kid, looking way up at Spock.

"Half-Vulcan." said Spock.

The kid bit his lip. "You help Uncle Khan." The kid gestured across the square. He grabbed Spock's hand and began pulling him in that direction. Kirk and Pike shared a look, and followed.

There was a man lying at the bottom of the steps. Pike took one look at him and hit his communicator, calling medical and requesting a team equipped for burns to the side steps of the Main Square.

It was bad. Multiple phaser burns to chest, leg and shoulder, with blood seeping from them and blood at his mouth. He was wearing a starfleet uniform with Commander's tabs, and had a pair of oversized sunglasses hanging haphazardly off one ear.

Spock meanwhile, had knelt down next to him, as did the kid, who poked his uncle. "Wake up, Uncle Khan. I found a Vulcan!" To their shock, the man opened his eyes and started talking. "Help... family... Marcus... Stop him."

"Don't try to talk," said Spock. "Help is on its way."

"He'll kill... family. Stop him."

"Stop who?" asked Kirk.

"Do you mean Admiral Alexander Marcus, head of Starfleet?" Pike asked. Alex was the best-known Marcus, after all.

"Yes."

"Is this to do with Section 31?" asked Pike.

The man nodded.

_Oh wonderful,_ thought Pike._ It looks like Marcus may well be up to something nasty. In any case, I need to know what is going on. _"Where are they?"

"Jup.." The man coughed and choked, closing his eyes and breathing shallowly once the coughing stopped.

"Admiral, it would perhaps be better to discuss this at a later time," said Spock. "Can I borrow your overtunics? He's going into shock.

"Ok, careful there. We can talk about this later." Pike sat down on the steps to remove his command tunic. The thin tunics wouldn't do much, but they'd be better than nothing.

"Jo... Vulcan." Khan's hand twitched towards the child. "23...1..7...4..." The man's eyes opened but they were glazed and promptly closed again. Spock checked his breathing - it was shallow but there.

The kid sniffled, and poked Khan's shoulder. "Uncle, wake up?"

"Medical help will be here shortly." said Spock, removing the boy's hand, who pulled away from Spock and glared. "They will help your Uncle."

"Admiral Marcus?"whispered Kirk to Pike, "He's accusing the head of Starfleet of wanting to kill his family!"

"And he's obviously been attacked by somebody," Pike whispered back.

The boy glared at them but didn't say anything.

"Do you know where your family is?" Spock asked the child. "And what is your name?"

The child turned back to Spock. "Jo."

"What is your full name?"

"Joachim Weiss."

Spock nodded. "Where are your parents?" The boy pointed at Khan.

"I believe you stated that Khan is your uncle."

Jo nodded.

"Where are your parents?" Spock asked again.

"They aren't my real parents. They're lying."

"Who aren't your real parents?" asked Spock, starting to look confused.

"These people who weren't my real mummy and daddy were taking care of me. They kept telling me to call them mummy and daddy but they're lying. They're Normals."

"Normal whats?" asked Kirk.

"Normals." said the boy, looking at them as if this should explain everything.

Finally the medical team arrived. They took Khan away with them. Jo tried to follow them, but Pike intervened. They didn't know what Admiral Marcus was up to, and the only person capable of answering questions right now was the little boy. Best to keep him with them until they had a better idea of what was going on.

"I want Uncle Khan!" Jo wailed, holding on grimly to Khan's arm. Spock pried him off. Jo squirmed and thrashed, screeching. Spock nearly dropped him, not expecting this reaction.

"But Uncle Khan wants you to stay with the Vulcan," said Pike, thinking swiftly. Khan had mentioned Vulcans... actually, it had sounded like he was trying to say something about the Vulcan embassy. Perhaps he had intended to seek refuge there? Not a bad idea, if he were in danger from Admiral Marcus and couldn't get out of Federation space.

Still, Pike would rather not disturb Ambassador Sarek until he had a better idea of what was going on. Starfleet needed to know what its leader was up to, and better to get that first-hand now than second-hand later from the Vulcans.

Jo seemed to calm a little, but glared like mad. "I want Uncle!"

"We also have some questions to ask you, so that we can better help Uncle Khan and the rest of your family." said Spock. "Khan's going to be sleeping for a while, so you wouldn't be able to talk to him anyway."

"I want to go home." He sniffled.

"Can you tell us where home is?"

Jo said nothing.

"Admiral, perhaps we should go back to your office or to the Enterprise. If this is likely to be politically delicate it might be better not to have Jo on Earth."

"The Enterprise is still Starfleet property. My apartment might be better, as it is not Starfleet property and most people would think twice before breaking in. I believe both of you are still on leave?"

"Yes" said Spock.

"Yeah," said Kirk. "But Chris, your apartment's still on Earth. You didn't sound all that surprised that Admiral Marcus was getting accused of something like this - what's up with that? I thought you two were friends."

"Long story. We need to know more as soon as possible. My place for now, and if we need to move later we can."

"Admiral, what about the Vulcan embassy? Khan may have intended to take refuge there," said Spock. "And it's Admiral Pike," he said, frowning at Kirk.

"Do you really want to wake Ambassador Sarek in the middle of the night if this turns out to be a minor internal Starfleet squabble?" asked Pike.

"Yeah, of course it's Admiral Pike," said Kirk. "You both knew I meant that, right?"

Pike rolled his eyes. Brilliant Jim Kirk might be, but the man definitely had subordination problems. He was beginning to wonder if the man would ever grow up.

"I'm hungry," said Jo. "Why's it night here? It was morning before."

"I'd be worried if it was morning after," said Jim.

"Let's go back to my apartment," said Pike. "You can have food there. I even have ice cream." Then he turned to Kirk. "We should really get the child checked out medically too. He doesn't look hurt, but given the state Khan was in we should check. Can Dr. McCoy be trusted with something like this?"

"Bones? Oh yeah."

"Can you find him and get him here?"

* * *

A/N: Thank you to everyone who reviewed. Special thanks to zedille for catching some spelling errors in the last chapter, and to a friend who prefers to remain anonymous for being a plot soundboard.


	11. Through the Eyes of a Child

Later, back at Pike's apartment and one small child appeased with ice cream, they continued the questions.

"So how did you get here?"

"Uncle Khan's yellow light machine put us here."

"Yellow light machine?"

"It made yellow light. And then there were weird people shooting at us. Uncle Khan knocked them down."

"And what happened to Uncle Khan?"

"The weird people shot him."

"Weird like us?"

"No, you're normal. They were wearing big orange suits." The child gestured with his ice cream and nearly lost some, meaning he had to stop to lick the dripping part.

Spock raised an eyebrow. "Hazmat suits? Were their faces covered with clear plastic?"

However, Jo just shrugged and licked his ice cream. "What's a hazmat suit?" he asked.

Eventually they managed to determine that:

-Khan had been attacked by people in hazmat suits

-They were previously on a section 31 base that was not located in the same time zone as San Fransisco, and that might not be on Earth.

-Pike and Kirk were 'Normals' but Jo and Khan weren't, although they weren't sure what Jo and Khan were

-Khan's last name was Singh, not Weiss

-They had mutual family who were asleep and were in Admiral Marcus' hands and endangered by him?

-Admiral Marcus had taken the child Jo away from his parents without giving a reason to the child when the child had at least one known living relative who wanted him.

-Khan was trying to do something involving the Vulcans, possibly seeking political asylum.

-Jo and Khan were both from somewhere with a warm climate, possibly India, but possibly not.

-They had arrived at the square by some sort of transporter that appeared to use Transwarp technology. Pike hadn't even known that such a device existed!

-Khan was severely injured and further information was likely to have to wait until he woke up.

It was at this point that Dr. McCoy arrived. He fussed over Jo, pronounced the kid fine physically and added a few more things to their list.

-If the boy was 31/2, then he was very advanced for his age.

-Jo had some bruises that looked to be a day or two old.

-Why did the kid bear biomarkers more normally found in GMO cows from the early 21st century?

-McCoy wanted to run further tests on the kid's genetics, but that would have to wait until he had access to a proper lab.

It was hard to know just what was going on. Pike was tempted to just call Alexander and ask him what the *$ was going on, but vetoed that idea when Kirk suggested it. If he really wanted to know what the Admiral was up to in Sector 31, he already knew he wasn't going to find out just by asking.

As soon as the Vulcan Embassy opened, they made their way there. Admiral Pike had always rather liked the Vulcan embassy, even if Sarek was a bit on the stiff side. It was beautiful and peaceful, making a change from the Academy and the students in particular. Not that there weren't undercurrents... the Vulcans had plenty of politics, even if they were handled politely and logically. And now he was about to saddle them with a three year old human. Poor Vulcans.

"Admiral Pike, Spock, Kirk." said the young Vulcan staff person who let them in. "Shall I let Ambassador Sarek know you have arrived?"

"Yes, please."

The Vulcan woman led them down a stone hallway to a waiting room, where they sat down. Except Jo, preferred to stand, alternating between peering at the historical artifacts in the display cabinets and looking around the room suspiciously.

After about five minutes wait they were all seated in Sarek's study. Pike explained the story, which received a raised eyebrow once or twice. "So I am to understand that you wish me to give this human child refuge from the head of your organization?"

"Just temporarily, until we have some idea of what is going on," said Pike.

"Will Admiral Marcus not object to this?"

"Father, this is a three year old human child, not a Vulcan one. He has no idea what is going on and has just seen his uncle almost die. He should not be trapped in the middle of this."

"Uncle Khan's not dead!" protested Jo. "You said he'd be all right. You promised!"

"Of course he isn't dead," reassured Kirk, poking Spock with his foot, presumably for being insensitive.

Sarek raised an eyebrow at Kirk and Spock's behavior. "I have no objection to the child staying here while you sort things out, if you truly believe such to be necessary. However, I am unsure what care a human child this age requires. As you pointed out, it is not the same as for a Vulcan child."

"Jim, you'll stay with Jo until the Vulcans are confident in how to look after him."

"Yes sir. But wouldn't Dr. McCoy be better? He has a child of his own."

"Me? Ambassador, do you have a genetics lab?" asked McCoy. "I need to run a few confidential tests on Jo."

"For most things, yes. Sometimes Vulcans on Earth have Vulcan-specific health issues humans know little of."

"Don't I know it. I'll stay with Jo for now, then. But after, I think I should help track down Khan in medical. Doctors talk more easily with another doctor."

"Spock, Kirk and I will be trying to determine what is going on here. You can join us once Jo is settled in, you've run the tests and got some conclusions." Pike, Kirk and Spock left, leaving McCoy with Jo and Sarek. Between them they ought to be able to look after one small boy.

About four hours later McCoy called from the hospital where he'd gone to find out about how Khan was doing. "He's gone." McCoy said bleakly. "Admiral Marcus turned up in person, demanded he be transferred and didn't tell anyone where he was taken. The doctors are complaining about protocol violations - and also about some very interesting things they noticed about Khan's DNA while he was there. I managed to get access to his records when I told them I was trying to find him at his nephew's request."

McCoy lowered his voice. "Dammit, Admiral, but I'm glad you've parked Jo with the Vulcans. We've got to do something: I think Section 31 may be trying to recreate the Augments."

Pike cursed, causing Spock to raise an eyebrow. "Marcus has taken Khan, and I don't know where." As for the speculation about the Augments, he kept that to himself for now.


	12. Consequences

**Chapter 11: Consequences**

A/N: Warning, this chapter contains dark themes, as well as deaths of minor characters. Let's just say that Admiral Marcus abandoned basic ethics a long time ago, and the main character and his family are at his mercy. There will be a short summary of this chapter at the beginning of the next.

* * *

Khan woke up in bed. After a few moments of confusion he realized he was in restraints. In a sickbay somewhere. And he didn't have his sunglasses. Not the most promising beginning, that.

Thinking back, he remembered the fight, the landing at Starfleet Academy and a Vulcan face leaning over him. Beyond that, he dimly remembered waking up in hospital somewhere once or twice. He breathed in deeply. No pain. That was good. But where was he? He couldn't tell.

At least not until he heard footsteps and saw Dr. Marin enter the room. Khan squeezed his eyes shut, feeling himself overwhelmed by horror. He was back in Admiral Marcus' hands. And his people - bar Jo - had never left at all.

"Now, there's no need for that Khan, or I suppose I should call you John shouldn't I? How are you doing today? You should be more or less functional again."

"If let me out restraints, I might know," said Khan.

"You're speaking much better than the last time I saw you, that is for certain. But I'll be keeping the restraints on, I believe. Admiral Marcus will be along shortly, and he wants a word with you." Dr. Marin ran a tricorder over him and hmmed thoughtfully at the output. "Well, you'll need to take it easy the next couple of days, but you're otherwise fine. No getting into battles with the security staff, now."

Khan sighed but said nothing. The doctor's sense of humor left much to be desired. The fool thought himself so clever... he reminded Khan a bit too much of some of the people who had created superhumans to do their dirty work and then assumed they would be able to control them. They'd been fools too.

"Oh, and you lost your glasses. I'll stick a pair here." Marin rummaged around in a desk and brought out a rather tatty-looking pair. "These aren't as good as your previous ones but they should still help. I'd imagine your visual issues have improved somewhat since you were last in my care?"

"Yes, but still need them."

Dr. Marin nodded and wrote something in his file before wandering out of the room.

It wasn't long before Admiral Marcus arrived, accompanied by six guards. He was furious, and made that obvious right from the beginning. "Hello John," he said, looming over Khan. "You will show how me how to remove the cryotubes from the torpedoes NOW."

"Yes, Sir." said Khan. Resistance would be futile right now. It would only anger Marcus more, and the fate of him and his people was on a knife edge as it was. The guards undid the restraints, and then snapped a metal collar around his neck. Khan frowned as he peered down, trying and failing to get a good look at it.

"That is to make sure you don't try anything stupid," said Admiral Marcus. "It will send a high dose of electricity through your body if triggered. A very high dose. It'd kill a normal person. With you, not sure. It will certainly take you down and keep you down. Might even cause more brain damage. Don't make me use it."

Khan nodded. A slave collar. In some ways, he'd been surprised Marcus hadn't taken a leaf out of Kim's book and stuck one on him on the first day. Not that he wanted one, but while their lack of precautions had made escape more possible - even if he'd still managed to mess it up! - it had also been a bit insulting.

He'd have to find a way to turn it off before he could do try again.

They walked to one of Marcus' classified storage rooms where the torpedoes and their precious passengers were being held. Khan felt numb, aware of stares from the people they passed, a few of whom had called him at least acquaintance, if not precisely friend.

At last they stood in the plain grey storage room, where three technicians waited for them. Khan told them how to open and safely remove the cryotubes from the torpedoes, then demonstrated. He noted that the capsule contained Joaquim Weiss, Joachim's father. He stepped back, letting the technicians open the others. The technicians opened the torpedoes and left.

All the while, Admiral Marcus stood watching silently. Now he spoke. "Well, Khan, what do you think I should do with you?"

Khan looked at him through narrowed eyes. It was probably a bad idea, but... "I would not done this if not fear for their lives in face your lies."

Marcus punched him in the face. Khan saw it coming and forced himself not to duck or return the blow with his bound hands. Marcus would look so much better if his features were rearranged... but he was in Marcus' power for now, however much that fact grated. The punch snapped his head back and stung, but otherwise didn't do much. Marcus shook his hand, visibly collecting himself before snarling instead:

"You dare blame me for your disobedience after getting some of my people killed trying to stop you? You arrogant bastard!"

"You may think yourself superior, but you are nothing here, nothing but my tool. You breathe only as long as you are useful. And as for your sleeping friends, I think you need an attitude adjustment if you want them to stay alive."

Marcus walked up to the cryotube containing Joaquim Weiss, holding one of the controls for Khan's collar casually in one hand.

"No!" cried Khan, taking a step forward.

Two of the guards pointed phasers at him, while Marcus and another guard had their fingers poised on the controls for his collar. Everyone froze.

"If you going punish me, punish me." said Khan, carefully not moving.

"Aren't I?" said Marcus. He pressed the button on the cryotube. The lights on the cryotube went out. Khan swayed, a red mist clouding his vision as his imagination depicted Marcus in small pieces. He dared not give in to his instincts now or they'd all die...

"You really do care for them," said Marcus, more softly. "Let's see how much." He moved on to the next cryotube.

"No," said Khan. "Use... collar." His hands were shaking.

"So you'd rather bear lots of physical pain yourself? Sorry, no dice." He pressed the button, killing Suzette.

"No... stop?"

"You killed 5 of my people Khan, in your little escape attempt. You'll have to come up with something better than that if you don't want me to kill at least that many of yours. And don't even think about attacking me. You kill me and both you and ALL of them will die."

Frantically Khan tried to figure out what Admiral Marcus could want from him other than to show him how helpless he was and humiliate him utterly. Suddenly Khan moved... and knelt. He lowered his eyes to the floor, waiting to see what came next. If the fool wanted him obedient and submissive, he'd show him that... right up until he killed him. Marcus had gone far beyond what he could ever forgive.

Admiral Marcus laughed. "You learn fast, don't you?" Khan dared look up.

"Not so fast, there. I'm going to be old-fashioned even by your times' standards and demand an oath. And you will address me as master."

Khan's eyes flashed. Since the Augments had overthrown those who created them they had called no merely-human 'master'. If those who followed him ever knew of this they would rip him apart. But if he did not there would be no Augments. He lowered his eyes. "Yes, master," said Khan slowly.

"Excellent," said Marcus. "Now repeat after me: I, Khan Noonian Singh do solemnly swear by that which I hold most dear..."

Khan carefully repeated his words. He didn't have any choice about refusing said oath. That didn't mean he'd keep it, for all that he normally valued his word.

"...to obey Admiral Alexander Marcus and those he appoints in authority over me. I will not attempt to rescue my people, family, comrades or whatever the hell I want to call them. I will not attempt to escape. So swear I, Khan Noonien Singh."

Khan remained kneeling and silent, looking at the floor until Admiral Marcus told him he could rise. Numbly, Khan rose and followed him.

The guards ushered him back to the cell he'd been kept in when he was an experimental subject. Khan sat down on the bed. What would happen now? He didn't know, but he did know that he had failed his people and himself. He needed to think, to plan, but for once he could think of nothing at all.


	13. Struggling With Puzzles

Summary of previous chapter:

Khan wakes up restrained in a hospital bed and realizes where he is when he sees Dr. Marin. Admiral Marcus arrives. He's furious, sticks electric collar on Khan, then gets Khan show the technicians how to get Khan's people out of the torpedoes. Aware of how tenuous his position is, Khan does so.

Marcus rants at Khan and hits him, then kills two of Khan's crew. Khan gets him to stop by kneeling and begging him to stop. Marcus then makes him swear that he won't try to rescue his family or escape himself. The guards then take Khan back to the cell where he first stayed when he'd been an experimental subject, leaving him wondering what was going to happen next.

Note: Zedille made useful suggestions, some of which I incorporated into the chapter. Thanks Zedille. Basic events have not changed.

Back to this chapter:

* * *

Meanwhile, Carol had woken up in the main Hanger of the Vengeance when medical personnel started fussing over her. She sat up, holding her painful head and trying to remember just what happened. John had attacked them? And something about her father...

Over the next couple of days, Carol pieced together a better picture of what exactly had happened. Five people dead at John's hands, others wounded or simply stunned with a phaser. And he'd kidnapped a little boy named Jo from the daycare center. Why? It was confusing, not least because a host of rumors appeared, most of which contradicted each other.

John was working for the Klingons, John had experienced a psychotic episode and thought he was Superman and Admiral Marcus was Lex Luthor, John wanted to sell the Vengeance to the Romulans for lots of money, John was going to join the Orion space pirates and give them Jo as a peace-offering, John was being blackmailed by someone... never let it be said that Section 31 was inadequate in the gossip category. Information was their stock-in-trade, after all.

She also took another look at John's file. There was no mention of any family, held hostage or otherwise. It was a rather empty file. In fact, there was precious little information on him before the accident, and even afterwards it seemed like there was a lot missing. Carol was willing to bet there was a more-classified file that told a lot more about John, and that some of the things in it wouldn't make for pleasant reading.

Admiral Marcus arrived within a couple of days and gave an official announcement: John had suffered a psychotic episode and/or severe flashback and was undergoing treatment in the secure section of Sickbay. No visitors allowed.

It was possible, but if it was true Carol suspected it would not have happened if John had not been pushed beyond his capabilities - beyond anyone's, really. She had warned her father, but did the man listen? And that would mean that the blood of the security team killed or injured was on her father's hands as surely as on John's.

If it wasn't true, and her father really was holding John's family hostage... she needed to find John's real file. People had died because something had gone awry. Whatever plan of her father's this was, it had gone too far. Her security clearance wasn't high enough, which meant she'd have to get hold of someone else's. And she had better not get caught.

* * *

Christopher Pike ground his teeth in frustration, then stopped, remembering that the dentist had told him he was damaging his teeth. It had been five days, and Khan had vanished without trace beyond him being in the care of Section 31.

They had had a bit more luck with getting information out of Jo. Dr. McCoy had analyzed the kid's DNA and Khan's in detail and had come to some very interesting conclusions. He'd also put the kid through a few tests - nothing invasive of course, the child was far too young to give informed consent and they didn't want to put him through more than he'd already endured. It was obvious that the kid was no stranger to medical curiosity and being poked and prodded.

Both Jo and Khan were both genetically altered, and not to prevent a genetic disease. The enhancements included sensory perception, strength, reflex times, intelligence, something to do with blood generation that fascinated McCoy, and disease resistance. Totally illegal, and likely to have cruel side-effects for those altered.

For one thing, Khan's need for sunglasses at night suggested that the sensory alterations had gone wrong in his case. Interestingly, apart from the augmentations, Khan and Jo did not appear to be closely related. But Khan's words allied with the alterations made Pike's blood turn cold.

The most obvious conclusion was that Admiral Marcus was trying to create something similar to the Augments of the late 20th century. Heck, Khan's name was even close to that of Khan Noonien Singh, the most powerful Augment leader! But surely that was ridiculous. Alex might be ruthless sometimes but he was nobody's fool, and everyone knew how well creating genetically engineered superhumans had turned out the last time. And in order to have already produced an adult, the program would have had to have been going for at least two decades unless they grew a lot faster than normal humans.

Whatever was going on, it must be stopped immediately before the damage got totally out of hand. That assumed that things weren't out of hand already. It wasn't as if Khan seemed terribly fond of those who sought to control him... Chris shook his head at his dark musings and thought what he could actually do.

He needed access to someone inside Section 31 to find out exactly what was really happening - and he'd better be prepared for the worst. For that, he'd need allies among the Starfleet brass, and access to more than the Enterprise.

He needed to contact Carol - she'd grown up calling him Uncle Chris, and she had always been more ethical than her father. He couldn't be sure she wouldn't simply report his interest to her father, but she was the best option he had. He didn't exactly know many people in Section 31 and asking Alex was obviously out of the question.

Carol was surprised to get a call from Uncle Chris, not that she called him that in public anymore. She was surprised to get a call from off-base, for that matter. Most of her friends didn't have the security clearance.

"Hi Uncle. It's been a while, what prompts this call?" She asked, leaning back in the armchair in her quarters.

"Thought it had been a long time since we last spoke. How are you?"

"Well enough, though things have been sort of rough lately."

"Oh? That doesn't sound good. Nothing world-breaking, I hope?"

"Oh no, just people problems. You stick a lot of people on one small station for months or years, working very hard on projects, and of course some of them will fall out with each other or even snap."

She wished she could tell him about the situation with John, but she doubted he was cleared to know the details of that - although for all she knew he might know more of it than she did. She wished she could ask him. For that matter, she might be able to find out if he knew Harrison from before.

"Have you met a Commander John Harrison? Tall, thin, black hair and pale skin."

"I can't say I have," said Chris. Then his eyes widened. "Does he wear sunglasses and have a nephew named Joachim Weiss?"

"He does wear sunglasses, but I don't know anything about a nephew."

"I might have met him under another name, but if so it was only briefly. Is this Harrison the person who snapped?"

"Uncle Chris, are you fishing for information?" asked Carol. If he didn't already know, it definitely wasn't up to her to tell him.

"What? Oh no, nothing you aren't allowed to tell me. But since you mentioned Harrison immediately after people snapping..."

"I suppose that would be a logical thing to think." Carol strongly suspected that seeking information is exactly what he was doing. What she didn't know was what information he was seeking, or why. Something involving Harrison, certainly. The man seemed to be at the center of an ever-increasing mystery. Gah! She hated not having all the pertinent information.

They returned to more innocent topics and soon ended the call, leaving Carol to brood on the little she had learned. John's more-classified information was likely under another name, but she had no idea what it was. On the other hand, she could go look up Joachim Weiss. Suddenly she gave a most unladylike snort. She didn't need to him up. When he left, John had kidnapped a small child named Jo.

Did that mean that Chris had run into Jo and John during John's aborted escape? It would explain why he was asking. And if Chris was worried enough to go fishing for information from her, then something was going on, likely something big. Something potentially career or even life ending for her, her father, Harrison and now this child Jo and maybe Chris as well. She was getting in way over her head.

But just because you were ignorant didn't mean something couldn't kill you.


	14. Who and What is John Harrison?

Carol had limited success working to backtrack and find out more of Harrison's past. It was careful and massively frustrating work. She still couldn't find his classified file, but she had managed to get a brief look at John's medical file. She'd assumed he'd been injured by a blow to the head or some kind of neurological disruptor weapon.

Apparently it was an accident in cryogenic revival. But cryogenics was rarely used these days, and when it was used it was almost error-free. Certainly free of mishaps causing brain-damage through oxygen deprivation! What had John been doing? Had he been revived by aliens or something?

Scenarios involving being revived by romulans or klingons bent on extracting information and having little care what happened to the human they'd caught flashed through her mind. Maybe she was being a bit over dramatic, but if anything like that had happened it was no wonder that John was having psychiatric problems.

If he was. Given that his name was likely not John Harrison, just who and what were they dealing with here?

She hadn't had time to do more than glance over the rest of the record. It was... short. Completely blank for anything before the past year, as if John had abruptly appeared, Athena-like, complete from that blasted cryotube. It didn't make any sense, since his service record stated that he'd been a Starfleet agent for two years by that point! Unless that was a lie. Given her father's cruel treatment of him, perhaps he was some sort of captive enemy? Someone who'd worked with Nero, even?

* * *

For Khan, days passed. Food was passed into his cell, but no one spoke to him, did anything to him, or gave him anything to do. The food also tasted odd, likely drugged. Khan stopped eating, but then they put it in the water. So much for that idea. He started eating again.

Khan wasn't quite sure what Marcus intended by this enforced inactivity. To make him aware how much he was in Marcus' power? Certainly. To convince him he was expendable and could be locked away permanently? Likely. Although if he were truly expendable Marcus would simply have had him killed. The man might mean to break him, but if he wanted to do that he'd be in for a disappointment.

Khan paced, made a half-dozen escape plans that all had problems with them, tried to meditate. He even sang a couple of times. He was bored, and he'd never dealt well with enforced mental and physical inactivity. Not that he'd really had the need before. There had always been people to fight, frighten, seduce or outwit, problems to solve, usually more things he needed to do than he really had time for. Now there was nothing to do but wait.

Time crawled by, and dark thoughts crept into the empty spaces. Joachim was an orphan now, and Khan had no idea where he was, or if he was even alive.

Once an emperor, now a prisoner, his own name seemed a mockery of all that he had once been. He had failed, and found himself boxed in with no way out. He should have stayed behind to die when the Botany left. That would at least have been an honorable end, and perhaps some new leader would have done better with this horrific situation. Someone with less baggage from the past.

When the thoughts came, Khan took to doing almost anything to distract himself, up to and including giving the camera in the corner the finger. He might also have punched a wall. But in the end, the thoughts always returned.

He moved less, lost in his own thoughts, and didn't pay much attention to his surroundings. It wasn't as if they changed, anyway, or as if what he did here mattered.

Then someone threw the door wide. Khan threw up his arm to protect his eyes, fumbling for his sunglasses. Finding them, he stood up and squinted at the figure silhouetted against the blinding light. Then he recognized Admiral Marcus' voice. "You're a mess," the Admiral said. "Go clean yourself up; I've got work for you to do."

How embarrassing. He realized suddenly that he hadn't had a proper shower or even a change of clothes since he'd been locked in. He must look and smell pretty bad.

And where had the dried blood on his right hand come from? He glanced at the wall and winced. Oh yes, that. He flexed his hand. Everything worked, but one of the bones in his middle finger had set less than straight and the finger was now slightly crooked.

Just under an hour later, a much tidier Khan met Admiral Marcus again. "You're going back to work," said the Admiral. "You'll be confined to your cell for off-hours, and will be accompanied at all times you are out of it by four guards. You'd better not cause trouble again, John Harrison, not if you want your precious family to survive."

Khan nodded silently. He needed out of that cell if he was to do anything productive. The Admiral handed him his PADD. "Don't even think about hacking this one," Admiral Marcus said. "It has extra precautions even you won't be able to crack. And you're banned from the rest of the base's computers." Again Khan nodded.

He followed Admiral Marcus dutifully back to the Vengeance. And his former team.

* * *

Carol was a bit surprised when she'd heard John was to be rejoining the team. That was going to be interesting. None of them had even been allowed to see him over the past week. Not that anyone other than her wanted to.

The mood on the team wasn't exactly in his favor. Al didn't want him to come back at all, protesting loudly that they didn't need him that badly. Maria, only recently out of her neck brace, curtly informed him it wasn't his choice and the man would be under guard and medicated to prevent any problems reoccurring.

Harrison arrived with Admiral Marcus just before 10 am. He somehow managed to look even more ghostly pale than before. Despite his known deadliness, he looked almost vulnerable. Instead of Connor, he had two guards. Carol was surprised to recognize one of them as one of her old classmates from the Academy. She hadn't seen Darren Smithson in ages. They'd have to catch up some time.

John was wearing a sort of thick coppery necklace - it looked a bit like those choker necklaces some teenage girls liked to wear a couple of years ago. Weird.

John stood at parade rest, expressionless and looking straight ahead as far as she could tell given his sunglasses.

"Commander Harrison will be guarded to prevent him becoming a threat in the event of a recurrence," said Admiral Marcus. "He's also on medication."

Carol wondered why her father was telling them this now, with Harrison present, when they already knew. After a few pleasantries, her father left, leaving John standing silent between his guards.

"Well, aren't you going to apologize?" demanded Al.

John turned slightly to look at him. "Sorry," said John slowly. "I not..."

"You don't what?" said Al, still glaring.

John shook his head but didn't speak.

Al took a step towards him, glaring.

"Al..." Maria began.

"John," said Carol, "can you remember the words?"

John shook his head.

"If you're sorry for hurting us and others, nod your head."

John nodded. "Sorry," he repeated.

Slowly, Al relaxed. "Suppose it isn't your fault if you didn't know what you were doing. What did you think was happening?"

John shook his head. "Family" was all he said.

"You said something about my father holding your family hostage," said Carol.

John tensed suddenly, and Carol took a step back, wondering if he was going to attack them or flee. "Be still," said Darren, grabbing John's shoulder. John stood very still.

"You sure you're well enough to be here?" asked Temujin. "You don't look so good."

"Why don't you get to work?" said the other guard. "He does better if he isn't reminded of his delusions." John nodded.

"In that case," said Maria, "let's get to work." Carol found herself volunteered to catch John up on what they had been doing in his absence. Not as much as should have been, to be honest. She'd been distracted, and Maria had been injured. There had been a big hole in the team without John, and none of them had really been functioning at their best.

As for functioning, John really wasn't doing well. She couldn't see what his eyes were doing, but he seemed really spaced out, and she wasn't getting much in the way of verbal answers, drawing out half his responses on his PADD. It was like he'd regressed to the early days in terms of language. What did her father think he was doing, making the man work when he was in this state! Was the man blind as well as heartless?

Or was John some sort of captive enemy, being forced to work for Starfleet? It would explain a lot. If so, Admiral Marcus' treatment of him was in contravention of half a dozen treaties on the treatment of enemy combatants. Of course, this was Section 31, where regular laws had a tendency to stretch to breaking point and sometimes beyond. Screw that.

"John, what is with the necklace?" Carol asked.

"Collar?" said John, touching the necklace. "Yes... control."

"It's just a precaution, Carol," said Darren.

"I see. I didn't think it looked like your fashion sense, John."

John raised his eyebrows. "Collar?... no." He gave a wry smile that she suspected didn't reach his eyes.

"Now we've managed to get the torpedoes slotted into the correct cradles on the Vengeance, but you need to tell me more about the details of how they work," said Carol, patting the side of the nearest torpedo. "And why these access ports are so big. You could fit a person in there with room to spare."

She wondered why John tensed. Darren did too, for that matter. What had she stumbled on this time?

As she watched John walk away between his guards at the end of the day, Carol found herself inwardly cursing the day she'd agreed to work in Section 31.


	15. Discord Reigns Supreme

She found Darren that evening in the mess. "Hey, Darren, why don't you come over here? I haven't seen you in ages."

"Sure," said Darren, balancing his tray in one hand as he came over. "I see you're a full-fledged weapons scientist now. How's that working for you?" He set his tray down, and pulled out a chair, which squeaked.

"Pretty well, for the most part," said Carol. "It's stressful sometimes. Have you been guarding long?"

Darren winced. "People, about four months. Before that it was sensitive and valuable objects for two months."

"How did you end up doing that? I thought you were on ship duty."

"I was on ship duty, but had a bit of a falling-out with some of my mates and a senior officer. Long story, but here I am."

Carol gave him a long look. It sounded like Darren's fondness for partying hard had finally bitten him in the rear. Hopefully he learned something from it - he had plenty of talent apart from that.

"Well, glad to see you, whatever the circumstances. Where's John?"

"In his cell. Cato's keeping an eye on him."

"Cell?"

"Oh, the high-security medical rooms sometimes get called that."

"Darren, I'm worried about your charge."

"Don't be, we've got him under control."

"It's not that I'm worried about so much. I know you're brilliant at hand-to-hand," said Carol. "John seems really out of it. While you're making sure he doesn't hurt others, who's making sure he's ok?"

"Uh Carol," said Darren. "This guy killed five people less than two weeks ago."

"Because he was out of his mind," said Carol. "I'm just asking if anyone is actually trying to improve his mental stability instead of getting the maximum amount of work out of him while preventing him from hurting others." She had to at least pretend she believed that was all that was going on. Maybe Darren knew more.

Darren was silent a moment. "Carol, that really isn't either of our jobs. And he's on medication."

"Then whose job is it, because they're doing a horrible job," said Carol, crossing her arms in front of her. "I dislike having my teammate attempt to steal the prototype, killing and injuring people in the process and stunning me. It's really bad for morale."

"That's one way to put it," said Al from four spaces along the table. "If he's so dangerous he has to be locked up and guarded constantly he has no business being around a top-secret weapons lab. The man's a menace and I want him gone."

Carol winced but couldn't really disagree.

"It's just precautionary," said Darren. "With the precautions we've got in place now he should be completely unable to do anyone any harm even if he were to try."

"Oh yeah?" said Al. "Would you recognize it if he rigged one of those damn torpedoes to go off in our faces? One of us is going to have to ride herd on him at all times, and it sure isn't going to be me."

"Carol, I think you'll be doing that," said Temujin. "You seem to be the only one of us who doesn't want to punch him every time he opens his mouth."

Al snorted and rolled his eyes. "I wonder why that is?"

"Because I'm a decent human being?" suggested Carol. Al could really be insufferable sometimes.

"No, because you think he's hot," said Al, smirking.

"Excuse me?" said Carol.

"Your eyes follow him whenever he walks into a room. You seek him out, ask after him when he's not there. It's blinding you-"

"I don't base my ethics on whether I find someone attractive," said Carol, face flaming. "And you're the one whose eyes follow any attractive female you see. Don't think I haven't noticed-"

"Ha! Then you do think he's cute. Temujin you owe me - "

Maria set her hand on Al's shoulder. "Al, Carol, stop it. You sound like thirteen year olds." She paused. "And yes, I could hear you clearly from the next table over."

"Who's going to babysit John, then? asked Temujin.

"I will," said Maria. "Now kindly change the subject or go elsewhere."

The rest of the meal continued quietly, with what comments there were being on other topics. As Carol left the hall, Darren stopped her. "Carol, about what you said earlier, can we talk privately?"

"Sure," said Carol.

They walked down to the hydroponic gardens, and sat down on a bench in the corner. The trickling of water and hum of the lights made white noise in the background. "About my charge... just how much do you know about him?"

"Not nearly as much as Al seems to believe," said Carol. She sighed. "Man's an idiot."

"Which one?"

"Both of them! John won't take help when offered and is afraid of something he won't talk about, and Al is just... Al. I don't really know John well. I don't think anyone here does, except possibly my father. What do you think of him?"

"John... your father... Carol, you aren't going to like some of what I have to say."

"I like being in the dark when people are getting killed a lot less."

"I can see that." said Darren, resting his chin on his hand. "The fact is, John isn't what he seems. He's dangerous."

"That much is obvious," said Carol. "What I want to know is why. His name isn't John Harrison either."

Darren's brows rose. "Carol, he's not psychotic."

"Is he a captive enemy combatant?"

Darren hesitated. "You could say that," he said. "I can't tell you everything, if the Admiral finds out I could die."

Something told Carol he wasn't exaggerating.

"Beware of your father. He's already killed people over this. Don't ask questions, especially not in public and not about Khan's family." Carol's stomach lurched. Now Darren was telling her her father had blood directly on his hands? But more immediately...

"Khan?"

Darren's expression told her he hadn't meant to tell her that. "He deserves what he's going through," he said, as if trying to convince himself. "Just stay away from him."

"Kind of hard to do that when he's my coworker. But I'll certainly keep your warnings in mind."

"Whatever you do, don't fall in love with him. The man is a killing machine."

"I am not so ruled by hormones as you and Al seem to think," snapped Carol. "I most definitely was wary of him before this and will be doubly so now, I simply needed to learn what was going on well enough to know what to do."

"Do you now?"

"For now, yes."

"Ok, let's talk about something else." But neither could think of much to say, so Darren left Carol sitting on the bench, thinking. It was true she did find John - Khan, rather, physically attractive. He was smart too, and charming when he wanted to be. If he had shown interest and wasn't so damaged and downright dangerous she might have been interested. As it was, no, she'd more sense, unlike some other women on the base she could name. They'd try and flirt with him and he'd completely ignore them.

Khan... at least she now had his real name to search under. She'd be careful around the man, certainly, but she was going to find out what was going on.


End file.
